unofficial mirror of help-guix@gnu.org 
 help / color / mirror / Atom feed
From: myglc2 <myglc2@gmail.com>
To: help-guix@gnu.org
Subject: R install.packages() fails: 'Peer certificate cannot be authenticated with given CA certificates'
Date: Thu, 29 Sep 2016 19:09:13 -0400	[thread overview]
Message-ID: <86fuoiwbfq.fsf@gmail.com> (raw)


With GuixSD user config ...

(use-package-modules
 base   ; glibc-utf8-locales
 ssh    ; mosh
 admin  ; tree
 aspell ; aspell-dict-en
 mail   ; notmuch mu isync
 statistics ; r
 emacs      ; emacs-ess
 certs      ; nss-certs
 )
(packages->manifest
 (list
  mosh
  tree
  aspell-dict-en ; because emacs doesn't find system install
  notmuch mu isync ; also building from git source but this gets run-time dependencies
  r emacs-ess
  r-devtools r-openssl r-stringr r-xml2 r-httr 
  )
 )

... if I try to install a CRAN package like this ...

install.packages("pROC")

... it fails like this ...

Warning: unable to access index for repository https://rweb.crmda.ku.edu/cran/src/contrib:
  cannot download all files
Warning messages:
1: In download.file(url, destfile = f, quiet = TRUE) :
  URL 'https://cran.r-project.org/CRAN_mirrors.csv': status was 'Peer certificate cannot be authenticated with given CA certificates'
2: package ‘pROC’ is not available (for R version 3.3.1) 

But if I "defeat" HTTPS like this ...

options(repos=
            c(
                CRAN = "http://cran.rstudio.com/"
            )
        )

... it works. I would prefer to use HTTPS, so here is the question:

How do I get R to present the CA certificates?

TIA - George

Full R session log is shown below.

***
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> options(STERM='iESS', str.dendrogram.last="'", editor='emacsclient', show.error.locations=TRUE)
> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C             
 [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8    
 [5] LC_MONETARY=en_US.utf8    LC_MESSAGES=en_US.utf8   
 [7] LC_PAPER=en_US.utf8       LC_NAME=C                
 [9] LC_ADDRESS=C              LC_TELEPHONE=C           
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C      

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     
> install.packages("pROC")
Installing package into ‘/home/g1/R/x86_64-unknown-linux-gnu-library/3.3’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
Warning: failed to download mirrors file (cannot download all files); using local file '/gnu/store/7543j3zkn95i7ixlc9fdq9hj0zrk5yq8-r-3.3.1/lib/R/doc/CRAN_mirrors.csv'
HTTPS CRAN mirror 

 1: 0-Cloud [https]                2: Austria [https]             
 3: Belgium (Ghent) [https]        4: Chile [https]               
 5: China (Beijing 4) [https]      6: Colombia (Cali) [https]     
 7: France (Lyon 1) [https]        8: France (Lyon 2) [https]     
 9: France (Paris 2) [https]      10: Germany (Münster) [https]   
11: Iceland [https]               12: Italy (Padua) [https]       
13: Japan (Tokyo) [https]         14: Mexico (Mexico City) [https]
15: New Zealand [https]           16: Russia (Moscow) [https]     
17: Spain (A Coruña) [https]      18: Spain (Madrid) [https]      
19: Switzerland [https]           20: UK (Bristol) [https]        
21: UK (Cambridge) [https]        22: USA (CA 1) [https]          
23: USA (KS) [https]              24: USA (MI 1) [https]          
25: USA (TN) [https]              26: USA (TX) [https]            
27: USA (WA) [https]              28: (HTTP mirrors)              


Selection: 23
Warning: unable to access index for repository https://rweb.crmda.ku.edu/cran/src/contrib:
  cannot download all files
Warning messages:
1: In download.file(url, destfile = f, quiet = TRUE) :
  URL 'https://cran.r-project.org/CRAN_mirrors.csv': status was 'Peer certificate cannot be authenticated with given CA certificates'
2: package ‘pROC’ is not available (for R version 3.3.1) 
> q("no")

Process R finished at Thu Sep 29 19:07:12 2016
***

             reply	other threads:[~2016-09-29 23:10 UTC|newest]

Thread overview: 5+ messages / expand[flat|nested]  mbox.gz  Atom feed  top
2016-09-29 23:09 myglc2 [this message]
2016-09-30  7:08 ` R install.packages() fails: 'Peer certificate cannot be authenticated with given CA certificates' Ricardo Wurmus
2016-09-30 14:12   ` curl_ca_bundle, and gnurl? ng0
2016-09-30 19:20     ` Ricardo Wurmus
2016-10-01 11:41       ` ng0

Reply instructions:

You may reply publicly to this message via plain-text email
using any one of the following methods:

* Save the following mbox file, import it into your mail client,
  and reply-to-all from there: mbox

  Avoid top-posting and favor interleaved quoting:
  https://en.wikipedia.org/wiki/Posting_style#Interleaved_style

  List information: https://guix.gnu.org/

* Reply using the --to, --cc, and --in-reply-to
  switches of git-send-email(1):

  git send-email \
    --in-reply-to=86fuoiwbfq.fsf@gmail.com \
    --to=myglc2@gmail.com \
    --cc=help-guix@gnu.org \
    /path/to/YOUR_REPLY

  https://kernel.org/pub/software/scm/git/docs/git-send-email.html

* If your mail client supports setting the In-Reply-To header
  via mailto: links, try the mailto: link
Be sure your reply has a Subject: header at the top and a blank line before the message body.
This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox;
as well as URLs for read-only IMAP folder(s) and NNTP newsgroup(s).